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Illumina announced updates to the Prep tab in BaseSpace that enable a couple of missing features for NextSeq users -- dual indexing and custom indexes. Also, we just received some new Mid-output kits and the Accessory Box now contains an additional 'dual index primer' reagent, which is to be added to well #18 when performing a run with dual indexes.
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Yep. They've changed the way dual indexing is done on on the NextSeq. BP10 is the primer to read the i5 index and needs to be added to #18 for all dual index runs. Our FAS told us paired end turnaround is carried out even on single read conformations in order to read the second index. The reason they switched is because the lack of dark cycles before the index read improves the read quality (less (pre)phasing) and therefore gives better assignment. The software must reverse compliment the i5 read because it's now reading from the other direction.
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